HHSearch: 7701 Segmentation fault (core dumped)

[cclough]

I'm getting an error on the hhsearch step:

Running hhsearch ./run_pipeline.sh: line 49: 7701 Segmentation fault (core dumped) $HH -i $WDIR/t000_.msa0.ss2.a3m -o $WDIR/t000_.hhr -v 0 > $WDIR/log/hhsearch.stdout 2> $WDIR/log/hhsearch.stderr

There's no output in hhsearch.stderr

It ran fine for T1078, but not for my 464aa protein.

Running the HHsearch step in isolation shows the following:

- 04:14:18.171 INFO: Searching 136710 database HHMs without prefiltering

- 04:14:18.221 INFO: Iteration 1

- 04:14:18.332 INFO: Scoring 136710 HMMs using HMM-HMM Viterbi alignment

- 04:14:18.614 INFO: Alternative alignment: 0

- 04:14:33.097 INFO: 136710 alignments done

- 04:14:33.333 INFO: Alternative alignment: 1

- 04:14:33.926 INFO: 3511 alignments done

- 04:14:33.929 INFO: Alternative alignment: 2

- 04:14:33.967 INFO: 188 alignments done

- 04:14:33.967 INFO: Alternative alignment: 3

- 04:14:33.982 INFO: 2 alignments done

Segmentation fault (core dumped)

I've tried things suggested elsewhere via google e.g. sudo sysctl vm.overcommit_memory=1, but no luck.

The protein returns a very large number of sequences from HHBlits. Initially it crashed there and I had to limit the MSA size with hhblits -maxseq 500

I have HHsearch v3.3.0

16 CPUs, 96GB memory. I've tried with more and less.

[jennifermbui]

Same here: the T1078 example ran fine but I also got the same problem for my sequence of only 200 aa. Have you @cclough figured out yet? Pls post the solutions if you know. Thanks!

[cclough]

@jennifermbui no still blocked on this

[jennifermbui]

@cclough, I actual installed HH-suite3 on my linux desktop rather using the command under miniconda. I'm sure that Sergey @lyskov and Ivan @gjoni would know why it broke. But, the name of the game is to produce t000_.hhr.

[ajrferrari]

I found the same issue and got in contact with the developers of hh-suite.
After tracing back the part of the code that was returning the segmentation fault, it seems PDB100 database does not contain an _a3m database which is required by the last hhsearch version.
Is it possible to make this database available with the PDB100 database?

[ajrferrari]

They added a flag which ignores the a3m missing file. Update your from source compiled version and add -premerge 0.

$HH -i $WDIR/t000_.msa0.ss2.a3m -o $WDIR/t000_.hhr -premerge 0

[jennifermbui]

Thanks for following up with hh-suite developers, @ajrferrari! @lyskov, I wonder if you would add to this flag to run_pipeline.sh. Also, I'm not sure why PDB100 does not contain an _a3m database. @aleaverfay @lyskov, Is it possible to make this database available with the PDB100 database? Thanks! Jen

[lyskov]

Thanks for following up with hh-suite developers, @ajrferrari! @lyskov, I wonder if you would add to this flag to run_pipeline.sh. Also, I'm not sure why PDB100 does not contain an _a3m database. @aleaverfay @lyskov, Is it possible to make this database available with the PDB100 database? Thanks! Jen

re flags addition and database alteration: tagging original authors @gjoni @minkbaek

[FrBonnardel]

The use of -premerge 0 also require to use hhsearch last version
available at https://github.com/soedinglab/hh-suite

[ajrferrari]

You can use the v3.3.0 if you compile from the github source. The premerge option was made available in the last couple days. Please pull the updated version.

…

On Thu, Jul 8, 2021 at 6:36 AM FrBonnardel ***@***.***> wrote: The use of -premerge 0 also require to use hhsearch last version — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFZL64PVNQ4TPWM342AKVKTTWWETHANCNFSM47BTNP2A> .

-- *Állan*

[menanagy01]

it still not working with me
It shows an error in :
" Running hhsearch
./run_pipeline.sh: line 57: 131266 Segmentation fault (core dumped) $HH -i $WDIR/t000_.msa0.ss2.a3m -o $WDIR/t000_.hhr -premerge 0 > $WDIR/log/hhsearch.stdout 2> $WDIR/log/hhsearch.stderr "

With the installed version HHsearch 3.3.0
Although it was worked well and outputs a result in an example T1078
my PC is core i7 and RAM 8G

[IL-6Li]

it still not working with me It shows an error in : " Running hhsearch ./run_pipeline.sh: line 57: 131266 Segmentation fault (core dumped) $HH -i $WDIR/t000_.msa0.ss2.a3m -o $WDIR/t000_.hhr -premerge 0 > $WDIR/log/hhsearch.stdout 2> $WDIR/log/hhsearch.stderr "

With the installed version HHsearch 3.3.0 Although it was worked well and outputs a result in an example T1078 my PC is core i7 and RAM 8G

i have the same problam ,can you tell me your solution？

[FrBonnardel]

Hi, it can be due to diverse issues including lack of memory, disk space, wrong version and corrupted patterns file.CheersLe 21 déc. 2023 06:06, giaoli ***@***.***> a écrit : it still not working with me It shows an error in : " Running hhsearch ./run_pipeline.sh: line 57: 131266 Segmentation fault (core dumped) $HH -i $WDIR/t000_.msa0.ss2.a3m -o $WDIR/t000_.hhr -premerge 0 > $WDIR/log/hhsearch.stdout 2> $WDIR/log/hhsearch.stderr " With the installed version HHsearch 3.3.0 Although it was worked well and outputs a result in an example T1078 my PC is core i7 and RAM 8G i have the same problam ,can you tell me your solution？ —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: ***@***.***>